<?xml version="1.0" encoding="UTF-8"?>

<gse xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:noNamespaceSchemaLocation="esquema-gcs.xsd">

^DATABASE = GeoMiame
!Database_name = Gene Expression Omnibus (GEO)
!Database_institute = NCBI NLM NIH
!Database_web_link = http://www.ncbi.nlm.nih.gov/geo
!Database_email = geo@ncbi.nlm.nih.gov
^SERIES = GSE93506
!Series_title = Coordinated regulation of acid resistance in Escherichia coli
!Series_geo_accession = GSE93506
!Series_status = Public on Jan 12 2017
!Series_submission_date = Jan 11 2017
!Series_last_update_date = Jan 25 2018
!Series_pubmed_id = 28061857
!Series_summary = We report regulatory interactions on four E. coli transcription factors in relation to the acid resistance systems by using a combination of ChIP-Seq and gene expression analysis
!Series_overall_design = Performed chromatin immunoprecipitation and total RNA extraction on WT strains cloned with inducible TFs in E. coli K-12 MG1655. Sequences were generated with an Illumina GAIIx
!Series_type = Expression profiling by high throughput sequencing
!Series_type = Genome binding/occupancy profiling by high throughput sequencing
!Series_contributor = Patricia,,Aquino
!Series_contributor = Brent,,Honda
!Series_contributor = Suma,,Jaini
!Series_contributor = Anna,,Lyubetskaya
!Series_contributor = Krutika,,Hosur
!Series_contributor = Joanna,G,Chiu
!Series_contributor = Iriny,,Ekladious
!Series_contributor = Dongjian,,Hu
!Series_contributor = Lin,,Jin
!Series_contributor = Marianna,K,Sayeg
!Series_contributor = Arion,I,Stettner
!Series_contributor = Julia,,Wang
!Series_contributor = Brandon,G,Wong
!Series_contributor = Winnie,S,Wong
!Series_contributor = Stephen,L,Alexander
!Series_contributor = Cong,,Ba
!Series_contributor = Seth,I,Bensussen
!Series_contributor = David,B,Bernstein
!Series_contributor = Dana,,Braff
!Series_contributor = Susie,,Cha
!Series_contributor = Daniel,I,Cheng
!Series_contributor = Jang,H,Cho
!Series_contributor = Kenny,,Chou
!Series_contributor = James,,Chuang
!Series_contributor = Daniel,E,Gastler
!Series_contributor = Daniel,J,Grasso
!Series_contributor = John,S,Greifenberger
!Series_contributor = Chen,,Guo
!Series_contributor = Anna,K,Hawes
!Series_contributor = Divya,V,Israni
!Series_contributor = Saloni,R,Jain
!Series_contributor = Jessica,,Kim
!Series_contributor = Junyu,,Lei
!Series_contributor = Hao,,Li
!Series_contributor = David,,Li
!Series_contributor = Qian,,Li
!Series_contributor = Christopher,P,Mancuso
!Series_contributor = Ning,,Mao
!Series_contributor = Salwa,F,Masud
!Series_contributor = Cari,L,Meisel
!Series_contributor = Jing,,Mi
!Series_contributor = Christine,S,Nyyforchyn
!Series_contributor = Minhee,,Park
!Series_contributor = Hannah,M,Peterson
!Series_contributor = Alfred,K,Ramirez
!Series_contributor = Daniel,S,Reynolds
!Series_contributor = Nae,G,Rim
!Series_contributor = Jared,C,Saffie
!Series_contributor = Hang,,Su
!Series_contributor = Wendell,R,Su
!Series_contributor = Yaqing,,Su
!Series_contributor = Meng,,Sun
!Series_contributor = Meghan,M,Thommes
!Series_contributor = Tao,,Tu
!Series_contributor = Nitinun,,Varongchayakul
!Series_contributor = Tyler,E,Wagner
!Series_contributor = Benjamin,H,Weinberg
!Series_contributor = Rouhui,,Yang
!Series_contributor = Anastasia,,Yaroslavsky
!Series_contributor = Christine,,Yoon
!Series_contributor = Yanyu,,Zhao
!Series_contributor = Alicia,J,Zollinger
!Series_contributor = Anne,M,Stringer
!Series_contributor = John,W,Foster
!Series_contributor = Joseph,,Wade
!Series_contributor = Sahadevan,,Raman
!Series_contributor = Natasha,,Broude
!Series_contributor = Wilson,W,Wong
!Series_contributor = James,E,Galagan
!Series_sample_id = GSM2453482
!Series_sample_id = GSM2453483
!Series_sample_id = GSM2453484
!Series_sample_id = GSM2453485
!Series_sample_id = GSM2453486
!Series_sample_id = GSM2453487
!Series_sample_id = GSM2667742
!Series_sample_id = GSM2667743
!Series_sample_id = GSM2667744
!Series_sample_id = GSM2667745
!Series_sample_id = GSM2667746
!Series_contact_name = James,,Galagan
!Series_contact_department = Biomedical Engineering
!Series_contact_institute = Boston University
!Series_contact_address = 44 Cummington Mall
!Series_contact_city = Boston
!Series_contact_state = MA
!Series_contact_zip/postal_code = 02115
!Series_contact_country = USA
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93506/suppl/GSE93506_RAW.tar
!Series_platform_id = GPL16227
!Series_platform_taxid = 83333
!Series_sample_taxid = 83333
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA360965
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP096575
^PLATFORM = GPL16227
!Platform_title = Illumina Genome Analyzer IIx (Escherichia coli K-12)
!Platform_geo_accession = GPL16227
!Platform_status = Public on Oct 31 2012
!Platform_submission_date = Oct 31 2012
!Platform_last_update_date = Oct 31 2012
!Platform_technology = high-throughput sequencing
!Platform_distribution = virtual
!Platform_organism = Escherichia coli K-12
!Platform_taxid = 83333
!Platform_contact_name = ,,GEO
!Platform_contact_country = USA
!Platform_data_row_count = 0
^SAMPLE = GSM2453482
!Sample_title = <Name>CsiR_ChIPSeq</Name>
!Sample_geo_accession = GSM2453482
!Sample_status = Public on Jan 12 2017
!Sample_submission_date = Jan 11 2017
!Sample_last_update_date = Jun 13 2017
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Culture cells
!Sample_organism_ch1 = <Orgn>Escherichia coli K-12</Orgn>
!Sample_taxid_ch1 = 83333
!Sample_characteristics_ch1 = strain: <Orgn>MG1655</Orgn>
!Sample_characteristics_ch1 = transcription factor: CsiR
!Sample_characteristics_ch1 = antibody: <Anti>anti-FLAG mAb</Anti>
!Sample_characteristics_ch1 = antibody vendor/catalog#: Sigma/Cat. No. F1804
!Sample_treatment_protocol_ch1 = For total RNA extraction, cells were pelleted in 4 °C.
!Sample_growth_protocol_ch1 = Cells were grown in <Med>LB media</Med> with <Supp>1mM IPTG</Supp> at <Temp>37 °C</Temp> with shaking for <Supp>2 hours</Supp>
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = For chromatin immunoprecipitation, cells were fixed with formaldehyde and glycine and sheared via sonication. Sheared DNA from lysate was immunoprecipitated (IP) out using an anti-FLAG mAb (Sigma). DNA was washed with IPP150 buffer and purified via ProteinaseK digestion and Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).
!Sample_extract_protocol_ch1 = Total RNA extraction was done using TRIzol reagent and DNAse digested. RNA purfication was carried out using Rneasy spin columns
!Sample_extract_protocol_ch1 = The appropriate protocols were performed using standard Illumina procedures
!Sample_data_processing = Basecalls performed using CASAVA version 1.8
!Sample_data_processing = Reads were aligned to GenBank ID U00096.2
!Sample_data_processing = Peak calling was done using SPAT
!Sample_data_processing = R scripts (Bioconductor GenomicRanges) and custom scripts were used to calculate RPKMs. Fold-change was calculated as ratio of RPKMs after TF induction to control experiment.
!Sample_data_processing = Genome_build: <Gversion>U00096.2</Gversion> (GenBank)
!Sample_data_processing = Supplementary_files_format_and_content: .xlsx files contain peak region locations and gene expression value for ChIP-Seq and RNA-Seq respectively
!Sample_platform_id = GPL16227
!Sample_contact_name = James,,Galagan
!Sample_contact_department = Biomedical Engineering
!Sample_contact_institute = Boston University
!Sample_contact_address = 44 Cummington Mall
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina Genome Analyzer IIx
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN06217846
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2485100
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2453nnn/GSM2453482/suppl/GSM2453482_CsiR_peaks.xlsx
!Sample_series_id = GSE93506
!Sample_data_row_count = 0
^SAMPLE = GSM2453483
!Sample_title = <Name>Nac_ChIPSeq</Name>
!Sample_geo_accession = GSM2453483
!Sample_status = Public on Jan 12 2017
!Sample_submission_date = Jan 11 2017
!Sample_last_update_date = Jun 13 2017
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Culture cells
!Sample_organism_ch1 = <Orgn>Escherichia coli K-12</Orgn>
!Sample_taxid_ch1 = 83333
!Sample_characteristics_ch1 = strain: <Orgn>MG1655</Orgn>
!Sample_characteristics_ch1 = transcription factor: Nac
!Sample_characteristics_ch1 = antibody: <Anti>anti-FLAG mAb</Anti>
!Sample_characteristics_ch1 = antibody vendor/catalog#: Sigma/Cat. No. F1804
!Sample_treatment_protocol_ch1 = For total RNA extraction, cells were pelleted in 4 °C.
!Sample_growth_protocol_ch1 = Cells were grown in <Med>LB media</Med> with <Supp>1mM IPTG</Supp> at <Temp>37 °C</Temp> with shaking for <Supp>2 hours</Supp>
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = For chromatin immunoprecipitation, cells were fixed with formaldehyde and glycine and sheared via sonication. Sheared DNA from lysate was immunoprecipitated (IP) out using an anti-FLAG mAb (Sigma). DNA was washed with IPP150 buffer and purified via ProteinaseK digestion and Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).
!Sample_extract_protocol_ch1 = Total RNA extraction was done using TRIzol reagent and DNAse digested. RNA purfication was carried out using Rneasy spin columns
!Sample_extract_protocol_ch1 = The appropriate protocols were performed using standard Illumina procedures
!Sample_data_processing = Basecalls performed using CASAVA version 1.8
!Sample_data_processing = Reads were aligned to GenBank ID U00096.2
!Sample_data_processing = Peak calling was done using SPAT
!Sample_data_processing = R scripts (Bioconductor GenomicRanges) and custom scripts were used to calculate RPKMs. Fold-change was calculated as ratio of RPKMs after TF induction to control experiment.
!Sample_data_processing = Genome_build: <Gversion>U00096.2</Gversion> (GenBank)
!Sample_data_processing = Supplementary_files_format_and_content: .xlsx files contain peak region locations and gene expression value for ChIP-Seq and RNA-Seq respectively
!Sample_platform_id = GPL16227
!Sample_contact_name = James,,Galagan
!Sample_contact_department = Biomedical Engineering
!Sample_contact_institute = Boston University
!Sample_contact_address = 44 Cummington Mall
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina Genome Analyzer IIx
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN06217851
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2485101
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2453nnn/GSM2453483/suppl/GSM2453483_Nac_peaks.xlsx
!Sample_series_id = GSE93506
!Sample_data_row_count = 0
^SAMPLE = GSM2453484
!Sample_title = <Name>NtrC_ChIPSeq</Name>
!Sample_geo_accession = GSM2453484
!Sample_status = Public on Jan 12 2017
!Sample_submission_date = Jan 11 2017
!Sample_last_update_date = Jun 13 2017
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Culture cells
!Sample_organism_ch1 = <Orgn>Escherichia coli K-12</Orgn>
!Sample_taxid_ch1 = 83333
!Sample_characteristics_ch1 = strain: <Orgn>MG1655</Orgn>
!Sample_characteristics_ch1 = transcription factor: NtrC
!Sample_characteristics_ch1 = antibody: <Anti>anti-FLAG mAb</Anti>
!Sample_characteristics_ch1 = antibody vendor/catalog#: Sigma/Cat. No. F1804
!Sample_treatment_protocol_ch1 = For total RNA extraction, cells were pelleted in 4 °C.
!Sample_growth_protocol_ch1 = Cells were grown in <Med>LB media</Med> with <Supp>1mM IPTG</Supp> at <Temp>37 °C</Temp> with shaking for <Supp>2 hours</Supp>
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = For chromatin immunoprecipitation, cells were fixed with formaldehyde and glycine and sheared via sonication. Sheared DNA from lysate was immunoprecipitated (IP) out using an anti-FLAG mAb (Sigma). DNA was washed with IPP150 buffer and purified via ProteinaseK digestion and Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).
!Sample_extract_protocol_ch1 = Total RNA extraction was done using TRIzol reagent and DNAse digested. RNA purfication was carried out using Rneasy spin columns
!Sample_extract_protocol_ch1 = The appropriate protocols were performed using standard Illumina procedures
!Sample_data_processing = Basecalls performed using CASAVA version 1.8
!Sample_data_processing = Reads were aligned to GenBank ID U00096.2
!Sample_data_processing = Peak calling was done using SPAT
!Sample_data_processing = R scripts (Bioconductor GenomicRanges) and custom scripts were used to calculate RPKMs. Fold-change was calculated as ratio of RPKMs after TF induction to control experiment.
!Sample_data_processing = Genome_build: <Gversion>U00096.2</Gversion> (GenBank)
!Sample_data_processing = Supplementary_files_format_and_content: .xlsx files contain peak region locations and gene expression value for ChIP-Seq and RNA-Seq respectively
!Sample_platform_id = GPL16227
!Sample_contact_name = James,,Galagan
!Sample_contact_department = Biomedical Engineering
!Sample_contact_institute = Boston University
!Sample_contact_address = 44 Cummington Mall
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina Genome Analyzer IIx
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN06217850
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2485102
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2453nnn/GSM2453484/suppl/GSM2453484_NtrC_peaks.xlsx
!Sample_series_id = GSE93506
!Sample_data_row_count = 0
^SAMPLE = GSM2453485
!Sample_title = <Name>OmpR_ChIPSeq</Name>
!Sample_geo_accession = GSM2453485
!Sample_status = Public on Jan 12 2017
!Sample_submission_date = Jan 11 2017
!Sample_last_update_date = Jun 13 2017
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Culture cells
!Sample_organism_ch1 = <Orgn>Escherichia coli K-12</Orgn>
!Sample_taxid_ch1 = 83333
!Sample_characteristics_ch1 = strain: <Orgn>MG1655</Orgn>
!Sample_characteristics_ch1 = transcription factor: OmpR
!Sample_characteristics_ch1 = antibody: <Anti>anti-FLAG mAb</Anti>
!Sample_characteristics_ch1 = antibody vendor/catalog#: Sigma/Cat. No. F1804
!Sample_treatment_protocol_ch1 = For total RNA extraction, cells were pelleted in 4 °C.
!Sample_growth_protocol_ch1 = Cells were grown in <Med>LB media</Med> with <Supp>1mM IPTG</Supp> at <Temp>37 °C</Temp> with shaking for <Supp>2 hours</Supp>
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = For chromatin immunoprecipitation, cells were fixed with formaldehyde and glycine and sheared via sonication. Sheared DNA from lysate was immunoprecipitated (IP) out using an anti-FLAG mAb (Sigma). DNA was washed with IPP150 buffer and purified via ProteinaseK digestion and Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).
!Sample_extract_protocol_ch1 = Total RNA extraction was done using TRIzol reagent and DNAse digested. RNA purfication was carried out using Rneasy spin columns
!Sample_extract_protocol_ch1 = The appropriate protocols were performed using standard Illumina procedures
!Sample_data_processing = Basecalls performed using CASAVA version 1.8
!Sample_data_processing = Reads were aligned to GenBank ID U00096.2
!Sample_data_processing = Peak calling was done using SPAT
!Sample_data_processing = R scripts (Bioconductor GenomicRanges) and custom scripts were used to calculate RPKMs. Fold-change was calculated as ratio of RPKMs after TF induction to control experiment.
!Sample_data_processing = Genome_build: <Gversion>U00096.2</Gversion> (GenBank)
!Sample_data_processing = Supplementary_files_format_and_content: .xlsx files contain peak region locations and gene expression value for ChIP-Seq and RNA-Seq respectively
!Sample_platform_id = GPL16227
!Sample_contact_name = James,,Galagan
!Sample_contact_department = Biomedical Engineering
!Sample_contact_institute = Boston University
!Sample_contact_address = 44 Cummington Mall
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina Genome Analyzer IIx
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN06217849
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2485103
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2453nnn/GSM2453485/suppl/GSM2453485_OmpR_peaks.xlsx
!Sample_series_id = GSE93506
!Sample_data_row_count = 0
^SAMPLE = GSM2453486
!Sample_title = <Name>CsiR_RNASeq</Name>
!Sample_geo_accession = GSM2453486
!Sample_status = Public on Jan 12 2017
!Sample_submission_date = Jan 11 2017
!Sample_last_update_date = Jun 13 2017
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Culture cells
!Sample_organism_ch1 = <Orgn>Escherichia coli K-12</Orgn>
!Sample_taxid_ch1 = 83333
!Sample_characteristics_ch1 = strain: <Orgn>MG1655</Orgn>
!Sample_characteristics_ch1 = transcription factor: CsiR
!Sample_treatment_protocol_ch1 = For total RNA extraction, cells were pelleted in 4 °C.
!Sample_growth_protocol_ch1 = Cells were grown in <Med>LB media</Med> with <Supp>1mM IPTG</Supp> at <Temp>37 °C</Temp> with shaking for <Supp>2 hours</Supp>
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = For chromatin immunoprecipitation, cells were fixed with formaldehyde and glycine and sheared via sonication. Sheared DNA from lysate was immunoprecipitated (IP) out using an anti-FLAG mAb (Sigma). DNA was washed with IPP150 buffer and purified via ProteinaseK digestion and Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).
!Sample_extract_protocol_ch1 = Total RNA extraction was done using TRIzol reagent and DNAse digested. RNA purfication was carried out using Rneasy spin columns
!Sample_extract_protocol_ch1 = The appropriate protocols were performed using standard Illumina procedures
!Sample_data_processing = Basecalls performed using CASAVA version 1.8
!Sample_data_processing = Reads were aligned to GenBank ID U00096.2
!Sample_data_processing = Peak calling was done using SPAT
!Sample_data_processing = R scripts (Bioconductor GenomicRanges) and custom scripts were used to calculate RPKMs. Fold-change was calculated as ratio of RPKMs after TF induction to control experiment.
!Sample_data_processing = Genome_build: <Gversion>U00096.2</Gversion> (GenBank)
!Sample_data_processing = Supplementary_files_format_and_content: .xlsx files contain peak region locations and gene expression value for ChIP-Seq and RNA-Seq respectively
!Sample_platform_id = GPL16227
!Sample_contact_name = James,,Galagan
!Sample_contact_department = Biomedical Engineering
!Sample_contact_institute = Boston University
!Sample_contact_address = 44 Cummington Mall
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina Genome Analyzer IIx
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = <Technique>RNA-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN06217848
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2485104
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2453nnn/GSM2453486/suppl/GSM2453486_CsiR_RNASeq.xlsx
!Sample_series_id = GSE93506
!Sample_data_row_count = 0
^SAMPLE = GSM2453487
!Sample_title = <Name>Nac_RNASeq</Name>
!Sample_geo_accession = GSM2453487
!Sample_status = Public on Jan 12 2017
!Sample_submission_date = Jan 11 2017
!Sample_last_update_date = Jun 13 2017
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Culture cells
!Sample_organism_ch1 = <Orgn>Escherichia coli K-12</Orgn>
!Sample_taxid_ch1 = 83333
!Sample_characteristics_ch1 = strain: <Orgn>MG1655</Orgn>
!Sample_characteristics_ch1 = transcription factor: Nac
!Sample_treatment_protocol_ch1 = For total RNA extraction, cells were pelleted in 4 °C.
!Sample_growth_protocol_ch1 = Cells were grown in <Med>LB media</Med> with <Supp>1mM IPTG</Supp> at <Temp>37 °C</Temp> with shaking for <Supp>2 hours</Supp>
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = For chromatin immunoprecipitation, cells were fixed with formaldehyde and glycine and sheared via sonication. Sheared DNA from lysate was immunoprecipitated (IP) out using an anti-FLAG mAb (Sigma). DNA was washed with IPP150 buffer and purified via ProteinaseK digestion and Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).
!Sample_extract_protocol_ch1 = Total RNA extraction was done using TRIzol reagent and DNAse digested. RNA purfication was carried out using Rneasy spin columns
!Sample_extract_protocol_ch1 = The appropriate protocols were performed using standard Illumina procedures
!Sample_data_processing = Basecalls performed using CASAVA version 1.8
!Sample_data_processing = Reads were aligned to GenBank ID U00096.2
!Sample_data_processing = Peak calling was done using SPAT
!Sample_data_processing = R scripts (Bioconductor GenomicRanges) and custom scripts were used to calculate RPKMs. Fold-change was calculated as ratio of RPKMs after TF induction to control experiment.
!Sample_data_processing = Genome_build: <Gversion>U00096.2</Gversion> (GenBank)
!Sample_data_processing = Supplementary_files_format_and_content: .xlsx files contain peak region locations and gene expression value for ChIP-Seq and RNA-Seq respectively
!Sample_platform_id = GPL16227
!Sample_contact_name = James,,Galagan
!Sample_contact_department = Biomedical Engineering
!Sample_contact_institute = Boston University
!Sample_contact_address = 44 Cummington Mall
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina Genome Analyzer IIx
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = <Technique>RNA-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN06217847
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2485105
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2453nnn/GSM2453487/suppl/GSM2453487_Nac_RNASeq.xlsx
!Sample_series_id = GSE93506
!Sample_data_row_count = 0
^SAMPLE = GSM2667742
!Sample_title = <Name>WT_ChIPSeq_1</Name>
!Sample_geo_accession = GSM2667742
!Sample_status = Public on Jun 14 2017
!Sample_submission_date = Jun 13 2017
!Sample_last_update_date = Jan 23 2018
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Culture cells
!Sample_organism_ch1 = <Orgn>Escherichia coli K-12</Orgn>
!Sample_taxid_ch1 = 83333
!Sample_characteristics_ch1 = strain: <Orgn>MG1655</Orgn>
!Sample_characteristics_ch1 = transcription factor: none (no vector)
!Sample_characteristics_ch1 = antibody: <Anti>anti-FLAG mAb</Anti>
!Sample_characteristics_ch1 = antibody vendor/catalog#: Sigma/Cat. No. F1804
!Sample_treatment_protocol_ch1 = For total RNA extraction, cells were pelleted in 4 °C.
!Sample_growth_protocol_ch1 = Cells were grown in <Med>LB media</Med> with <Supp>1mM IPTG</Supp> at <Temp>37 °C</Temp> with shaking for <Supp>2 hours</Supp>
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = For chromatin immunoprecipitation, cells were fixed with formaldehyde and glycine and sheared via sonication. IP was carried out using an anti-FLAG mAb.
!Sample_extract_protocol_ch1 = Total RNA extraction was done using TRIzol reagent and DNAse digested. RNA purfication was carried out using Rneasy spin columns
!Sample_extract_protocol_ch1 = The appropriate protocols were performed using standard Illumina procedures
!Sample_data_processing = Basecalls performed using CASAVA version 1.8
!Sample_data_processing = Reads were aligned to GenBank ID U00096.2
!Sample_data_processing = Peak calling was done using SPAT
!Sample_data_processing = R scripts (Bioconductor GenomicRanges) and custom scripts were used to calculate RPKMs. Fold-change was calculated as ratio of RPKMs after TF induction to control experiment.
!Sample_data_processing = Genome_build: <Gversion>U00096.2</Gversion> (GenBank)
!Sample_data_processing = Supplementary_files_format_and_content: text file with peak calls
!Sample_platform_id = GPL16227
!Sample_contact_name = James,,Galagan
!Sample_contact_department = Biomedical Engineering
!Sample_contact_institute = Boston University
!Sample_contact_address = 44 Cummington Mall
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina Genome Analyzer IIx
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07229896
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2916189
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2667nnn/GSM2667742/suppl/GSM2667742_WT_73_regions.txt.gz
!Sample_series_id = GSE93506
!Sample_data_row_count = 0
^SAMPLE = GSM2667743
!Sample_title = <Name>WT_ChIPSeq_2</Name>
!Sample_geo_accession = GSM2667743
!Sample_status = Public on Jun 14 2017
!Sample_submission_date = Jun 13 2017
!Sample_last_update_date = Jan 23 2018
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Culture cells
!Sample_organism_ch1 = <Orgn>Escherichia coli K-12</Orgn>
!Sample_taxid_ch1 = 83333
!Sample_characteristics_ch1 = strain: <Orgn>MG1655</Orgn>
!Sample_characteristics_ch1 = transcription factor: none (no vector)
!Sample_characteristics_ch1 = antibody: <Anti>anti-FLAG mAb</Anti>
!Sample_characteristics_ch1 = antibody vendor/catalog#: Sigma/Cat. No. F1804
!Sample_treatment_protocol_ch1 = For total RNA extraction, cells were pelleted in 4 °C.
!Sample_growth_protocol_ch1 = Cells were grown in <Med>LB media</Med> with <Supp>1mM IPTG</Supp> at <Temp>37 °C</Temp> with shaking for <Supp>2 hours</Supp>
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = For chromatin immunoprecipitation, cells were fixed with formaldehyde and glycine and sheared via sonication. IP was carried out using an anti-FLAG mAb.
!Sample_extract_protocol_ch1 = Total RNA extraction was done using TRIzol reagent and DNAse digested. RNA purfication was carried out using Rneasy spin columns
!Sample_extract_protocol_ch1 = The appropriate protocols were performed using standard Illumina procedures
!Sample_data_processing = Basecalls performed using CASAVA version 1.8
!Sample_data_processing = Reads were aligned to GenBank ID U00096.2
!Sample_data_processing = Peak calling was done using SPAT
!Sample_data_processing = R scripts (Bioconductor GenomicRanges) and custom scripts were used to calculate RPKMs. Fold-change was calculated as ratio of RPKMs after TF induction to control experiment.
!Sample_data_processing = Genome_build: <Gversion>U00096.2</Gversion> (GenBank)
!Sample_data_processing = Supplementary_files_format_and_content: text file with peak calls
!Sample_platform_id = GPL16227
!Sample_contact_name = James,,Galagan
!Sample_contact_department = Biomedical Engineering
!Sample_contact_institute = Boston University
!Sample_contact_address = 44 Cummington Mall
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina Genome Analyzer IIx
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07229900
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2916190
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2667nnn/GSM2667743/suppl/GSM2667743_WT_77_regions.txt.gz
!Sample_series_id = GSE93506
!Sample_data_row_count = 0
^SAMPLE = GSM2667744
!Sample_title = <Name>pT7_ChIPSeq_1</Name>
!Sample_geo_accession = GSM2667744
!Sample_status = Public on Jun 14 2017
!Sample_submission_date = Jun 13 2017
!Sample_last_update_date = Jan 23 2018
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Culture cells
!Sample_organism_ch1 = <Orgn>Escherichia coli K-12</Orgn>
!Sample_taxid_ch1 = 83333
!Sample_characteristics_ch1 = strain: <Orgn>MG1655</Orgn>
!Sample_characteristics_ch1 = transcription factor: none (empty vector)
!Sample_characteristics_ch1 = antibody: <Anti>anti-FLAG mAb</Anti>
!Sample_characteristics_ch1 = antibody vendor/catalog#: Sigma/Cat. No. F1804
!Sample_treatment_protocol_ch1 = For total RNA extraction, cells were pelleted in 4 °C.
!Sample_growth_protocol_ch1 = Cells were grown in <Med>LB media</Med> with <Supp>1mM IPTG</Supp> at <Temp>37 °C</Temp> with shaking for <Supp>2 hours</Supp>
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = For chromatin immunoprecipitation, cells were fixed with formaldehyde and glycine and sheared via sonication. IP was carried out using an anti-FLAG mAb.
!Sample_extract_protocol_ch1 = Total RNA extraction was done using TRIzol reagent and DNAse digested. RNA purfication was carried out using Rneasy spin columns
!Sample_extract_protocol_ch1 = The appropriate protocols were performed using standard Illumina procedures
!Sample_data_processing = Basecalls performed using CASAVA version 1.8
!Sample_data_processing = Reads were aligned to GenBank ID U00096.2
!Sample_data_processing = Peak calling was done using SPAT
!Sample_data_processing = R scripts (Bioconductor GenomicRanges) and custom scripts were used to calculate RPKMs. Fold-change was calculated as ratio of RPKMs after TF induction to control experiment.
!Sample_data_processing = Genome_build: <Gversion>U00096.2</Gversion> (GenBank)
!Sample_data_processing = Supplementary_files_format_and_content: text file with peak calls
!Sample_platform_id = GPL16227
!Sample_contact_name = James,,Galagan
!Sample_contact_department = Biomedical Engineering
!Sample_contact_institute = Boston University
!Sample_contact_address = 44 Cummington Mall
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina Genome Analyzer IIx
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07229899
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2916191
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2667nnn/GSM2667744/suppl/GSM2667744_PT7_73_regions.txt.gz
!Sample_series_id = GSE93506
!Sample_data_row_count = 0
^SAMPLE = GSM2667745
!Sample_title = <Name>pT7_ChIPSeq_2</Name>
!Sample_geo_accession = GSM2667745
!Sample_status = Public on Jun 14 2017
!Sample_submission_date = Jun 13 2017
!Sample_last_update_date = Jan 23 2018
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Culture cells
!Sample_organism_ch1 = <Orgn>Escherichia coli K-12</Orgn>
!Sample_taxid_ch1 = 83333
!Sample_characteristics_ch1 = strain: <Orgn>MG1655</Orgn>
!Sample_characteristics_ch1 = transcription factor: none (empty vector)
!Sample_characteristics_ch1 = antibody: <Anti>anti-FLAG mAb</Anti>
!Sample_characteristics_ch1 = antibody vendor/catalog#: Sigma/Cat. No. F1804
!Sample_treatment_protocol_ch1 = For total RNA extraction, cells were pelleted in 4 °C.
!Sample_growth_protocol_ch1 = Cells were grown in <Med>LB media</Med> with <Supp>1mM IPTG</Supp> at <Temp>37 °C</Temp> with shaking for <Supp>2 hours</Supp>
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = For chromatin immunoprecipitation, cells were fixed with formaldehyde and glycine and sheared via sonication. IP was carried out using an anti-FLAG mAb.
!Sample_extract_protocol_ch1 = Total RNA extraction was done using TRIzol reagent and DNAse digested. RNA purfication was carried out using Rneasy spin columns
!Sample_extract_protocol_ch1 = The appropriate protocols were performed using standard Illumina procedures
!Sample_data_processing = Basecalls performed using CASAVA version 1.8
!Sample_data_processing = Reads were aligned to GenBank ID U00096.2
!Sample_data_processing = Peak calling was done using SPAT
!Sample_data_processing = R scripts (Bioconductor GenomicRanges) and custom scripts were used to calculate RPKMs. Fold-change was calculated as ratio of RPKMs after TF induction to control experiment.
!Sample_data_processing = Genome_build: <Gversion>U00096.2</Gversion> (GenBank)
!Sample_data_processing = Supplementary_files_format_and_content: text file with peak calls
!Sample_platform_id = GPL16227
!Sample_contact_name = James,,Galagan
!Sample_contact_department = Biomedical Engineering
!Sample_contact_institute = Boston University
!Sample_contact_address = 44 Cummington Mall
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina Genome Analyzer IIx
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07229898
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2916192
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2667nnn/GSM2667745/suppl/GSM2667745_PT7_77_regions.txt.gz
!Sample_series_id = GSE93506
!Sample_data_row_count = 0
^SAMPLE = GSM2667746
!Sample_title = <Name>WT_RNASeq</Name>
!Sample_geo_accession = GSM2667746
!Sample_status = Public on Jun 14 2017
!Sample_submission_date = Jun 13 2017
!Sample_last_update_date = Jun 14 2017
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Culture cells
!Sample_organism_ch1 = <Orgn>Escherichia coli K-12</Orgn>
!Sample_taxid_ch1 = 83333
!Sample_characteristics_ch1 = strain: <Orgn>MG1655</Orgn>
!Sample_characteristics_ch1 = transcription factor: none (no vector)
!Sample_characteristics_ch1 = antibody: <Anti>anti-FLAG mAb</Anti>
!Sample_characteristics_ch1 = antibody vendor/catalog#: Sigma/Cat. No. F1804
!Sample_treatment_protocol_ch1 = For total RNA extraction, cells were pelleted in 4 °C.
!Sample_growth_protocol_ch1 = Cells were grown in <Med>LB media</Med> with <Supp>1mM IPTG</Supp> at <Temp>37 °C</Temp> with shaking for <Supp>2 hours</Supp>
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = For chromatin immunoprecipitation, cells were fixed with formaldehyde and glycine and sheared via sonication. IP was carried out using an anti-FLAG mAb.
!Sample_extract_protocol_ch1 = Total RNA extraction was done using TRIzol reagent and DNAse digested. RNA purfication was carried out using Rneasy spin columns
!Sample_extract_protocol_ch1 = The appropriate protocols were performed using standard Illumina procedures
!Sample_description = Processed data (RPKM) for this sample are included in the files located on GSM2453486 and GSM2453487.
!Sample_data_processing = Basecalls performed using CASAVA version 1.8
!Sample_data_processing = Reads were aligned to GenBank ID U00096.2
!Sample_data_processing = Peak calling was done using SPAT
!Sample_data_processing = R scripts (Bioconductor GenomicRanges) and custom scripts were used to calculate RPKMs. Fold-change was calculated as ratio of RPKMs after TF induction to control experiment.
!Sample_data_processing = Genome_build: <Gversion>U00096.2</Gversion> (GenBank)
!Sample_data_processing = Supplementary_files_format_and_content: text file with peak calls
!Sample_platform_id = GPL16227
!Sample_contact_name = James,,Galagan
!Sample_contact_department = Biomedical Engineering
!Sample_contact_institute = Boston University
!Sample_contact_address = 44 Cummington Mall
!Sample_contact_city = Boston
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02115
!Sample_contact_country = USA
!Sample_instrument_model = Illumina Genome Analyzer IIx
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = <Technique>RNA-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07229897
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2916193
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE93506
!Sample_data_row_count = 0

</gse>